Contacts of the strand formed by residues 198 - 204 (chain C) in PDB entry 1FSK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C LEU* 3.9 24.9 - - + -
159C TRP* 3.6 28.9 - - + -
160C ASN* 3.4 14.1 - - - +
164C LEU* 4.3 13.7 - - + -
186C VAL* 5.0 2.7 - - + -
188C VAL* 5.2 9.2 - - + -
192C THR 5.8 1.3 - - - +
193C TRP* 4.1 22.6 - - + +
196C GLU* 4.1 2.1 + - + -
197C THR* 1.3 80.0 + - - +
199C THR* 1.3 69.8 + - - +
214C LYS* 3.6 5.9 - - - +
215C ILE* 3.0 25.9 + - + +
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C TRP* 3.4 6.3 - - - -
160C ASN* 2.6 55.2 + - - +
161C SER* 6.1 0.2 - - - +
197C THR* 4.6 7.6 - - - +
198C VAL* 1.3 82.3 - - - +
200C CYS* 1.3 63.1 + - - +
201C ASN* 3.7 7.2 + - - +
212C ASP* 4.2 7.4 - - - +
213C LYS 2.9 24.7 + - - -
214C LYS* 3.7 10.8 + - + +
215C ILE 4.3 1.1 - - - +
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Residues in contact with CYS 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C VAL* 4.4 6.3 - - - -
145C CYS* 2.6 43.7 - - - -
157C VAL* 5.8 4.5 - - + -
158C THR 3.3 7.4 - - - +
159C TRP* 3.5 26.8 - - + +
199C THR* 1.3 73.1 + - - +
201C ASN* 1.3 60.4 + - - +
202C VAL* 5.2 4.0 - - - +
211C VAL 3.7 1.2 - - - +
212C ASP* 3.3 4.7 - - - -
213C LYS* 3.0 43.4 + - - -
215C ILE* 5.1 0.7 - - - -
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Residues in contact with ASN 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C THR* 3.8 1.2 + - - +
157C VAL* 3.3 3.5 - - - -
158C THR* 2.5 68.8 + - - +
160C ASN* 3.5 1.9 - - - +
161C SER* 2.5 45.1 + - - +
199C THR* 3.7 11.6 + - - +
200C CYS* 1.3 74.4 - - - +
202C VAL* 1.3 62.6 + - - +
203C ALA* 4.0 0.9 + - - +
210C LYS* 5.9 6.1 - - + -
212C ASP* 3.2 23.8 - - - +
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Residues in contact with VAL 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C PRO* 4.9 6.3 - - + -
126C VAL* 3.6 36.6 - - + -
145C CYS* 6.0 0.7 - - - -
147C VAL* 3.6 32.8 - - + -
155C VAL* 4.2 12.6 - - + -
156C THR 3.5 7.9 - - - +
157C VAL* 4.1 11.4 - - + +
200C CYS* 3.8 6.2 - - - +
201C ASN* 1.3 74.5 - - - +
203C ALA* 1.3 64.0 + - - +
204C HIS 4.5 0.2 + - - -
210C LYS* 3.5 3.4 - - - +
211C VAL* 2.8 54.3 + - + +
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Residues in contact with ALA 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C VAL* 3.3 7.0 - - - +
156C THR* 2.6 54.5 + - + +
201C ASN 5.2 1.3 - - - +
202C VAL* 1.3 74.8 - - - +
204C HIS* 1.3 60.1 + - - +
205C PRO* 3.8 6.8 - - + +
209C THR 3.8 4.7 - - - +
210C LYS* 3.6 32.8 - - + +
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Residues in contact with HIS 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C THR 3.8 7.9 - - - -
123C PRO* 4.4 0.2 - - + -
124C PRO* 3.8 20.6 - - + +
150C TYR* 3.6 10.0 - + - -
151C PHE 3.4 19.2 - - - -
152C PRO 2.9 22.6 + - - -
154C PRO 3.4 20.2 - - - -
155C VAL* 3.5 17.9 - - + -
203C ALA* 1.3 70.5 - - - +
205C PRO* 1.3 71.8 - - - +
206C ALA* 3.4 20.1 - - + +
207C SER* 2.6 43.5 + - - +
209C THR* 3.0 27.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il